Gov. Jan Brewer after a news conference last week about uninvestigated cases within Arizona’s Child Protective Services agency. She asked a team of legislators, prosecutors, child welfare advocates and state officials to identify poor practices within the agency.Credit
Ross D. Franklin/Associated Press

PHOENIX — A longtime homicide detective on assignment with Arizona’s child welfare agency noticed an unfamiliar notation — N.I., for not investigated — as he examined a file containing allegations of sibling-on-sibling sexual abuse. When he encountered the notation again, on a file listing accusations that a father burned his son with an iron, the detective began asking questions.

In all, a review of the agency uncovered 6,554 such files, all wrongfully shelved before any type of investigation was started, out of malice or neglect by whoever handled them, officials said.

The revelations come as caseworkers at the agency, Child Protective Services, have been taking on a record number of cases regarding child neglect or abuse. Among the shelved files were 5,000 reports made in the last 20 months to a child welfare hotline that Gov. Jan Brewer had taken credit for reorganizing.

The scandal, unusual even for an agency plagued by decades of problems, threatens to deal a setback to Ms. Brewer’s administration and her legacy, which her advisers have hoped would be about much more than her record on immigration. After pushing an expansion of Medicaid through the Legislature despite heavy opposition from fellow Republicans, Ms. Brewer had hoped to focus on getting more money for well-performing public schools, which have been crippled by several years of budget cuts.

Instead, she finds herself deflecting criticism of and fielding calls for the resignation of Clarence H. Carter, her handpicked director of the Department of Economic Security, whose broad portfolio encompasses dozens of safety-net programs, including child welfare. “There must be accountability in this matter, and I will insist on further reforms to make sure it cannot happen again,” she said in a statement last month.

Tackling the child welfare agency’s problems could be a thorny endeavor, given that Ms. Brewer must balance a slow economic recovery against the needs of child protection and other agencies that offer essential services, all of which are contending for a piece of the financial pie.

Some say the situation could present an opportunity.

“For the governor, this isn’t just a matter of policy,” said Barrett Marson, a public affairs consultant who worked for several years for the Republican majority in the Legislature. “This is a legacy-building project.”

Unlike with an earlier crisis — when 73 children died from abuse and neglect from 1997 to 2002, including many whose cases had been closed — the needs seem to go beyond money. This time, there is an almost pervasive sense that Child Protective Services requires a profound overhaul — a “wrecking ball,” as Laurie Roberts, a columnist for The Arizona Republic who has long chronicled the agency’s troubles, wrote last week.

“Inevitably they’ll say they need more resources, and they may, but there’s something else that’s needed, and that’s a change in the culture of this agency,” Rick Romley, a former Maricopa County official who commissioned a report in 2003 examining the problems of Child Protective Services. “Unless you have a major change in the way they do business, we’re going to continue to see these scandals come about.”

Mending the agency has ranked among Ms. Brewer’s priorities, but lasting results have eluded her. In January, in her State of the State address, she took credit for reforming the hotline system that had closed thousands of neglect and abuse calls without further study. But it was the investigative unit she established last year that uncovered the ignored cases.

About 2,000 calls were assessed over three days last month. Last week, she asked a team of legislators, prosecutors, child welfare advocates and state officials to oversee the investigation of each of the calls that had not been investigated, and to identify poor practices within the agency. But on Friday, team members ordered that the cases be re-examined after learning that some of the same people who could have been involved in shelving the calls were taking part in the review.

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State Senator Nancy Barto, a Republican who is co-chairwoman of the Child Protective Services Legislative Oversight Committee, said many problems stemmed from a sense that no one was accountable in an agency that is part of the largest bureaucracy in state government. Its director, Mr. Carter, who managed the federal food stamp program under President George W. Bush, oversees cash assistance and health care benefits, services for the elderly and the developmentally disabled, employment training, and refugee resettlement, among many other programs.

“They have in a lot of ways an impossible job to do perfectly, but that shouldn’t explain their failure to fix what needs to be fixed,” Ms. Barto said.

Already, the child welfare agency has a backlog of 10,000 cases and an additional 12,000 whose investigations, started in the last budget year, have not been completed, according to an analysis by Children’s Action Alliance, one of the largest advocacy groups in the state. The reports of neglect increased by 36 percent from October 2007 to last March, and more children died as a result of maltreatment last year (70) than in 2007 (60), the analysis said. The agency says it has roughly 600 fewer caseworkers than what it would need to meet caseload standards.

Dana Wolfe Naimark, president and chief executive of the Children’s Action Alliance, said the challenges facing the agency were made worse by budget cuts during the recent recession, which ended many preventive services intended to help families before children are removed from their homes. Child care subsidies for working parents remain frozen, cuts to rates paid to child care providers have not been restored, and the money appropriated from federal grants for cash assistance programs continues to be directed to the agency’s general budget.

Although much of the financing that Child Protective Services lost since 2009 has been restored, “the workload is still far larger than the agency is structured to handle, and I believe that’s the root cause of the problems going on right now,” Ms. Naimark said.

She and many others are waiting to see what Ms. Brewer will propose in the coming legislative session. Though well intentioned, the changes the governor has supported so far “have clearly not been enough to fundamentally change the agency and avoid another crisis,” Ms. Naimark said.

A version of this article appears in print on December 11, 2013, on Page A19 of the New York edition with the headline: Thousands of Ignored Abuse Allegations Plague Arizona Welfare Agency. Order Reprints|Today's Paper|Subscribe